An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. Export

@article{citeulike:118686, abstract = {Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base-pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure.}, address = {Department of Chemistry, California Institute of Technology, Pasadena, California 91125, USA.}, author = {Dirks, R. M. and Pierce, N. A.}, citeulike-article-id = {118686}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.20057}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15139042}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15139042}, day = {30}, doi = {10.1002/jcc.20057}, issn = {0192-8651}, journal = {J Comput Chem}, keywords = {acide-base, base-pairing}, month = {July}, number = {10}, pages = {1295--1304}, posted-at = {2008-02-23 15:43:34}, priority = {3}, title = {An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.}, url = {http://dx.doi.org/10.1002/jcc.20057}, volume = {25}, year = {2004} }

TY - JOUR ID - citeulike:118686 L3 - citeulike-article-id:118686 N2 - Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base-pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure. IS - 10 JF - J Comput Chem SN - 0192-8651 AD - Department of Chemistry, California Institute of Technology, Pasadena, California 91125, USA. EP - 1304 TI - An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. VL - 25 SP - 1295 KW - acide-base KW - base-pairing AU - Dirks, RM AU - Pierce, NA PY - 2004/07/30/ UR - http://dx.doi.org/10.1002/jcc.20057 ER -